The Peculiarities of Large Intron Splicing in Animals

In mammals a considerable 92% of genes contain introns, with hundreds and hundreds of these introns reaching the incredible size of over 50,000 nucleotides. These “large introns” must be spliced out of the pre-mRNA in a timely fashion, which involves bringing together distant 5′ and 3′ acceptor and donor splice sites. In invertebrates, especially Drosophila, it has been shown that larger introns can be spliced efficiently through a process known as recursive splicing—a consecutive splicing from the 5′-end at a series of combined donor-acceptor splice sites called RP-sites. Using a computational analysis of the genomic sequences, we show that vertebrates lack the proper enrichment of RP-sites in their large introns, and, therefore, require some other method to aid splicing. We analyzed over 15,000 non-redundant, large introns from six mammals, 1,600 from chicken and zebrafish, and 560 non-redundant large introns from five invertebrates. Our bioinformatic investigation demonstrates that, unlike the studied invertebrates, the studied vertebrate genomes contain consistently abundant amounts of direct and complementary strand interspersed repetitive elements (mainly SINEs and LINEs) that may form stems with each other in large introns. This examination showed that predicted stems are indeed abundant and stable in the large introns of mammals. We hypothesize that such stems with long loops within large introns allow intron splice sites to find each other more quickly by folding the intronic RNA upon itself at smaller intervals and, thus, reducing the distance between donor and acceptor sites

Scholarly research productivity among ophthalmology residency graduates

Purpose: The Accreditation Council for Graduate Medical Education (ACGME) requires that ophthalmology residents participate in scholarly activity during residency. However, to our knowledge it is unknown whether research publications during undergraduate, medical school, residency or fellowship training predict future academic publication performance among ophthalmologists. The aim of this study was to (1) measure scholarly research productivity (as measured by the H-index) among ophthalmology residency graduates, as measured by peer-reviewed publication output, and its relation to future publication output, and (2) evaluate whether scholarly impact of academic ophthalmologists is correlated with any specific characteristics.Methods: This study is cross-sectional in nature and included a random sample of 50 ophthalmology residency programs. From each program, a list of graduating residents from years 2013, 2014, and 2015 was compiled and each graduate was search on Scopus, PubMed, and Google Scholar. The publications of each graduate were then identified and data was extracted and collected in a double blind, duplicate fashion by 2 investigators. Research publication output was then stratified and analyzed.Results: Graduates that had a higher mean total publication (M = 9.11, SD=12.91) were significantly more likely to pursue a fellowship than those that did not (M=2.68, SD=3.16) (t234= -3.9, p = .0001). Graduates with more first person publications and higher H-index values were also significantly more likely to pursue fellowships (t234= -3.78, p = 0.0002) (t234= -3.93, p = 0.0001).Graduates that had a higher mean total publication (M = 14.2, SD= 18.19) were more likely to pursue academic careers than those that did not (M=4.57, SD = 4.88) (t234= -6.3, p = 0 .0001). Graduates with more first person publications and higher H-index values were also significantly more likely to pursue academic careers (t234= -5.17, p = 0.001) (t234= -4.84, p <0.0001). Gender proved to not be a significant determination of research pursuit in terms of publication or first person publication numbers (t234= -1.01, p = .3107) (t234= -0.53, p = .5949). However, H-index values for men (M = 3.06, SD= 3.47 ) and women (M = 2.52, SD=2.64) were significantly different (t234= -3.9, p = 0.0406).Conclusion: The positive correlation between the between graduates' research productivity and career and future research outcomes could present an interesting aspect for viewing candidates for fellowship or careers. The correlation demonstrates that students who performed research before and during residency were more productive with research after residency. This could present a positive reason to select an individual for a fellowship or academic program. The lack of research conversely indicates a likelihood of low research productivity. This could potentially negatively impact candidates. The evaluation of an individual's H-value, first-person publications, or total number of publications can then possibly be supplementary for decision making or gauge potential

Critical association of ncRNA with introns

It has been widely acknowledged that non-coding RNAs are master-regulators of genomic functions. However, the significance of the presence of ncRNA within introns has not received proper attention. ncRNA within introns are commonly produced through the post-splicing process and are specific signals of gene transcription events, impacting many other genes and modulating their expression. This study, along with the following discussion, details the association of thousands of ncRNAs—snoRNA, miRNA, siRNA, piRNA and long ncRNA—within human introns. We propose that such an association between human introns and ncRNAs has a pronounced synergistic effect with important implications for fine-tuning gene expression patterns across the entire genome

Exploiting mid-range DNA patterns for sequence classification: binary abstraction Markov models

Messenger RNA sequences possess specific nucleotide patterns distinguishing them from non-coding genomic sequences. In this study, we explore the utilization of modified Markov models to analyze sequences up to 44 bp, far beyond the 8-bp limit of conventional Markov models, for exon/intron discrimination. In order to analyze nucleotide sequences of this length, their information content is first reduced by conversion into shorter binary patterns via the application of numerous abstraction schemes. After the conversion of genomic sequences to binary strings, homogenous Markov models trained on the binary sequences are used to discriminate between exons and introns. We term this approach the Binary Abstraction Markov Model (BAMM). High-quality abstraction schemes for exon/intron discrimination are selected using optimization algorithms on supercomputers. The best MM classifiers are then combined using support vector machines into a single classifier. With this approach, over 95% classification accuracy is achieved without taking reading frame into account. With further development, the BAMM approach can be applied to sequences lacking the genetic code such as ncRNAs and 5′-untranslated regions

Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures

<p>Abstract</p> <p>Background</p> <p>Genomes possess different levels of non-randomness, in particular, an inhomogeneity in their nucleotide composition. Inhomogeneity is manifest from the short-range where neighboring nucleotides influence the choice of base at a site, to the long-range, commonly known as isochores, where a particular base composition can span millions of nucleotides. A separate genomic issue that has yet to be thoroughly elucidated is the role that RNA secondary structure (SS) plays in gene expression.</p> <p>Results</p> <p>We present novel data and approaches that show that a mid-range inhomogeneity (~30 to 1000 nt) not only exists in mammalian genomes but is also significantly associated with strong RNA SS. A whole-genome bioinformatics investigation of local SS in a set of 11,315 non-redundant human pre-mRNA sequences has been carried out. Four distinct components of these molecules (5'-UTRs, exons, introns and 3'-UTRs) were considered separately, since they differ in overall nucleotide composition, sequence motifs and periodicities. For each pre-mRNA component, the abundance of strong local SS (< -25 kcal/mol) was a factor of two to ten greater than a random expectation model. The randomization process preserves the short-range inhomogeneity of the corresponding natural sequences, thus, eliminating short-range signals as possible contributors to any observed phenomena.</p> <p>Conclusion</p> <p>We demonstrate that the excess of strong local SS in pre-mRNAs is linked to the little explored phenomenon of genomic mid-range inhomogeneity (MRI). MRI is an interdependence between nucleotide choice and base composition over a distance of 20–1000 nt. Additionally, we have created a public computational resource to support further study of genomic MRI.</p

Novel and Extendable Genotyping System For Human Respiratory Syncytial Virus Based On Whole-Genome Sequence analysis

BACKGROUND: Human respiratory syncytial virus (RSV) is one of the leading causes of respiratory infections, especially in infants and young children. Previous RSV sequencing studies have primarily focused on partial sequencing of G gene (200-300 nucleotides) for genotype characterization or diagnostics. However, the genotype assignment with G gene has not recapitulated the phylogenetic signal of other genes, and there is no consensus on RSV genotype definition. METHODS: We conducted maximum likelihood phylogenetic analysis with 10 RSV individual genes and whole-genome sequence (WGS) that are published in GenBank. RSV genotypes were determined by using phylogenetic analysis and pair-wise node distances. RESULTS: In this study, we first statistically examined the phylogenetic incongruence, rate variation for each RSV gene sequence and WGS. We then proposed a new RSV genotyping system based on a comparative analysis of WGS and the temporal distribution of strains. We also provide an RSV classification tool to perform RSV genotype assignment and a publicly accessible up-to-date instance of Nextstrain where the phylogenetic relationship of all genotypes can be explored. CONCLUSIONS: This revised RSV genotyping system will provide important information for disease surveillance, epidemiology, and vaccine development

Convergent amino acid signatures in polyphyletic Campylobacter jejuni subpopulations suggest human niche tropism

Human infection with the gastrointestinal pathogen Campylobacter jejuni is dependent upon the opportunity for zoonotic transmission and the ability of strains to colonize the human host. Certain lineages of this diverse organism are more common in human infection but the factors underlying this overrepresentation are not fully understood. We analyzed 601 isolate genomes from agricultural animals and human clinical cases, including isolates from the multihost (ecological generalist) ST-21 and ST-45 clonal complexes (CCs). Combined nucleotide and amino acid sequence analysis identified 12 human-only amino acid KPAX clusters among polyphyletic lineages within the common disease causing CC21 group isolates, with no such clusters among CC45 isolates. Isolate sequence types within human-only CC21 group KPAX clusters have been sampled from other hosts, including poultry, so rather than representing unsampled reservoir hosts, the increase in relative frequency in human infection potentially reflects a genetic bottleneck at the point of human infection. Consistent with this, sequence enrichment analysis identified nucleotide variation in genes with putative functions related to human colonization and pathogenesis, in human-only clusters. Furthermore, the tight clustering and polyphyly of human-only lineage clusters within a single CC suggest the repeated evolution of human association through acquisition of genetic elements within this complex. Taken together, combined nucleotide and amino acid analysis of large isolate collections may provide clues about human niche tropism and the nature of the forces that promote the emergence of clinically important C. jejuni lineages.Peer reviewe

Evolution of genomic sequence inhomogeneity at mid-range scales

<p>Abstract</p> <p>Background</p> <p>Mid-range inhomogeneity or MRI is the significant enrichment of particular nucleotides in genomic sequences extending from 30 up to several thousands of nucleotides. The best-known manifestation of MRI is CpG islands representing CG-rich regions. Recently it was demonstrated that MRI could be observed not only for G+C content but also for all other nucleotide pairings (e.g. A+G and G+T) as well as for individual bases. Various types of MRI regions are 4-20 times enriched in mammalian genomes compared to their occurrences in random models.</p> <p>Results</p> <p>This paper explores how different types of mutations change MRI regions. Human, chimpanzee and <it>Macaca mulatta </it>genomes were aligned to study the projected effects of substitutions and indels on human sequence evolution within both MRI regions and control regions of average nucleotide composition. Over 18.8 million fixed point substitutions, 3.9 million SNPs, and indels spanning 6.9 Mb were procured and evaluated in human. They include 1.8 Mb substitutions and 1.9 Mb indels within MRI regions. Ancestral and mutant (derived) alleles for substitutions have been determined. Substitutions were grouped according to their fixation within human populations: fixed substitutions (from the human-chimp-macaca alignment), major SNPs (> 80% mutant allele frequency within humans), medium SNPs (20% - 80% mutant allele frequency), minor SNPs (3% - 20%), and rare SNPs (<3%). Data on short (< 3 bp) and medium-length (3 - 50 bp) insertions and deletions within MRI regions and appropriate control regions were analyzed for the effect of indels on the expansion or diminution of such regions as well as on changing nucleotide composition.</p> <p>Conclusion</p> <p>MRI regions have comparable levels of de novo mutations to the control genomic sequences with average base composition. De novo substitutions rapidly erode MRI regions, bringing their nucleotide composition toward genome-average levels. However, those substitutions that favor the maintenance of MRI properties have a higher chance to spread through the entire population. Indels have a clear tendency to maintain MRI features yet they have a smaller impact than substitutions. All in all, the observed fixation bias for mutations helps to preserve MRI regions during evolution.</p

What are patients asking about shoulder arthroplasty? An investigation of Google searches

Introduction: The utilization of shoulder arthroplasty has been increasing steadily over the last few decades. Given this continuous increase, we expect that patients will increasingly search the internet for sources of information regarding shoulder arthroplasty. The primary objective of this study is to characterize the content of the most frequently asked questions (FAQs) regarding shoulder arthroplasty. The secondary objective is to assess both the quality and transparency of the suggested information for shoulder arthroplasty.Methods: On October 9th, 2022 the following search terms were searched using Google “shoulder arthroplasty”, “total shoulder arthroplasty”, “reverse shoulder arthroplasty”, and “reverse shoulder surgery.” For each search the “people also ask” function was queried until a minimum of 150 FAQs were generated for each search term. We recorded the individual FAQs along with the linked answer sources. All FAQs were classified using the Rothwell Classification. All sources were assessed for transparency using JAMA Benchmark and quality with the Brief DISCERN tool.Results section: Our search returned a total of 1275 FAQs. After removing duplicates and unrelated FAQs our included sample size was 173. Fact questions were the most common classification type (102/173, 59%) followed by value questions (52/173,30%) and policy questions (19/173, 11.0%). The most common fact questions were related to technical details (42/103, 40.7%). Medical Practices (67/173, 38.7%) were the most encountered source type followed by Academic sources(60/173, 34.6%). Both Academic and Medical Practices were associated with poor transparency (Table 1.). The one-way analysis of variance (ANOVA) revealed a significant difference in mean quality scores among the 5 source types (F = 18.6, P <.001) with Medical Practices averaging the lowest score (16.1/30) compared to Commercial sources which were found to have the highest quality of all included sources (24.1/30). (Table 1)Discussion: Patients seeking online information for shoulder arthroplasty appear to search Google for questions related to a plethora of technical details and restrictions. The most common source type encountered by patients are those of Medical Practices; these were found to have both poor quality as well as poor transparency as measured by JAMA Benchmark and Brief DISCERN. Our study has several limitations, JAMA benchmark and Brief DISCERN do not assess the accuracy of the information. Secondly, our study is cross-sectional and cannot be generalizable to other fields or other topics. Lastly, this study assessed online sources from one moment in time. Given the large amount of internet traffic Google experiences, web sources provided by the platform may change with time and search trends. Moving forward, medical practices should use validated tools as guidance for increasing the transparency and quality of the medical information they publish online. Physicians should know that their patients may be informing themselves about shoulder arthroplasty risks and management with low quality internet sources. Our findings reinforce the importance of well informed, evidence-based patient counseling before and after shoulder arthroplasty